The fabrication of semiconductor devices, such as logic and memory devices, typically includes processing a substrate such as a semiconductor wafer using a large number of semiconductor fabrication processes to form various features and multiple levels of the semiconductor devices. As semiconductor device size become smaller and smaller, it becomes critical to develop enhanced inspection and review devices and procedures. One such inspection technology includes electron beam based inspection systems, such as, scanning electron microscopy (SEM). In a single beam SEM, performing focus adjustments involves taking multiple images at different focus settings, and then choosing the best image (or interpolating between images to find the best focus). Frequently, astigmatism correction is also adjusted, which can further increase the number of images required. The time to acquire images can be relatively long, which reduces availability of the inspection tool. It would be advantageous to provide a multi-beam SEM system and method that cures the shortcomings observed in single beam SEM approaches.